Claude Skills by HolobiomicsLab

Use when after formatting raw mass spectrometry transition data into

Use when when preparing to run compound metadata enrichment or structure

Use when after a CNN model has generated predicted molecular embeddings

Use when you have calculated pairwise mass differences from MS peaks

Use when after computing expected adduct ions for a metabolite using

Use when when you have isolated, high-confidence reference chromatographic

Use when when you have IM-MS lipidomics data with measured CCS values

Use when when you have a processed mass spectrum object (e.g., from Bruker

Use when when performing m/z domain calibration on FT-ICR or high-resolution

Use when you have training LC-HRMS chromatograms (rt × m/z matrix format)

Use when you have executed a structure annotation pipeline (like BAM)

Use when when you have curated structure-organism pairs with associated

Use when when applying sequential filters to a large metabolomics peak

Use when when you have PSM files (output from search engines like MaxQuant,

Use when when you have a metabolomics metadata table and need to automatically

Use when after fitting linear regression models to relate peak area intensities

'Use when when you have trained multiple regression models (e.g., using

Use when you have trained two or more regression models (e.g., original

'Use when you have model predictions and ground-truth labels for a test

Use when after training a regression model on labeled continuous data

Use when when you have trained a regression model on experimental retention

Use when after training a deep-learning regression model (e.g., for CCS

Use when you have a labeled dataset of molecular structures with experimental

Use when when you have fitted one or more regression models (linear or

Use when after training or fine-tuning a retention time prediction model

Use when after generating collision cross section predictions on a validation

Use when you have matched multiomics measurements (CNV, mutations, DNA

Use when after generating a frequency count table (e.g., from count_fold_changes

Use when when you have raw count tables from 16S rRNA sequencing (microbiome)

Use when after applying a normalization method (e.g., median scaling,

Use when apply this filter when working with MS-DIAL peak lists (feature

Use when you have a peak table from XCMS preprocessing with intensity

Use when when you have preprocessed metabolomics data with pooled QC

Use when when a software project has reached a stable milestone (v-tagged

'Use when you need to validate that a software project''s release branch

Use when when preparing a release branch for a Maven-based project (like

Use when when you have implemented the same visualization (e.g., chromatogram,

Use when you have an imputed, long-format metabolomics dataset with repeated

Use when when you have metabolomics data organised across multiple experimental

Use when after NMR or MS data acquisition and preprocessing (phasing,

Use when after frequency-based denoising has been applied to individual

Use when you have multiple MS/MS spectra (replicates) for a single metabolic

Use when after extracting raw MS/MS spectra from mzML files for individual

Use when you need to validate that a scientific software project's continuous

Use when when you have a USI string (e.g., 'mzspec:GNPS:TASK-abc123:scan:1943')

Use when you have a GitHub repository URL, a documented Python version

Use when when you need to deploy a containerized scientific tool (e.g.,

Use when when starting a fresh ENPKG installation, you have a GitHub

Use when you need to set up a development environment for a project that

Use when you have identified a published method (e.g., MIST-CF for chemical